* "Kalinka" is Russian for "snowball tree" and there's a famous folk song about it. "Malinka" is Russian for "raspberry," is mentioned in Kalinka, and also happens to be Polish for "hickey."
Freud is Sigmund Freud, founder of psychoanalysis, who notably claimed human behavior stems from sexual and aggressive urges. A keloid is a type of scar. A marade is a march combined with a parade.
** CLICK FOR PRETENTIOUS! ANALYSIS

Well, huh. I think I'm going to take Hachi's off-hand comment on Twitter about his goal of drawing Riding Hoodie to be "fairytale-y [and] sexually charming" and pretty much run with that. (Okay, well, it's not like that's the only thing I have to go off of.)
The "message [Mikushka's] thought about much too much" is probably related to admission of love or proposal - she has nobody to give it to at the moment, though she's "always" been trying to get the chance, it seems.
The way "before we drop to just one" is written in Japanese ("1-nin," not "hitori," though the latter IS how it's sung), it seems unlikely that it's talking about a couple of "two" turning to "one." Rather, it has to do with taking away layers, matryoshka style.
Mikushka wants to know all her partner's layers, to "deep down," but is worried because a) what will she find? b) she'll probably have to show her deepest layers too, or - probably most likely - c) getting "deep down" will involve sex.
(Given all the layer symbolism, it's probably worth nothing that Mikushka and Riding Hoodie are pretty bundled up. Not sure if you can make much of Mikushka's 'phones, though.)
Riding Hoodie (a part/layer of Mikushka or a representation of her peers) starts pressuring Mikushka to "rendezvous" with her partner, wink wink, nudge nudge. Her Little Red Riding Hood + wolf design is pretty appropriate for this role.
(Nico suggested the more innocuous answer of "rendezvous" simply meaning "date," but I'd definitely say things are more serious than being too shy to ask him on a date. Unless that date leads to an "adventure," of course...)
The hands staying at 4 is likely related to Mikushka's being unable to "truly" mature until she can overcome the obstacle of sexual intimacy. (Or at least, Riding Hoodie would have her believe that makes her mature.)
"Dancing" either refers to continuing the relationship sans passion or the act of "dancing around" the issue of sex itself. Which are kinda one and the same, I suppose.
Mikushka eventually seems to be swayed by Riding Hoodie and asks her partner if they should "do more fantastic things," but he tells her to "wait." You can be the judge of whether or not she ends up listening to him, though. Smooch, smooch.
524 can be read "Konishi." Which could refer to composer Yasuharu Konishi (who calls his record label 524), Saki Konishi from Persona 4 (you know, true selves and all that? Eh?), or Mitsuki Konishi from The World Ends With You. Cough.
This theory is certainly clever, at least: 524 skips over 1 and 3. There's "no 13." Read that Japanese-style, and there's "no imi." Translate that word, and there's "no meaning." (That mostly supports Nicopedia's theory that Hachi is basically trolling them for trying to interpret his songs.)
Looking at it from a more English angle (which is decently probable considering it's sung that way), it could mean "five TO four," signifying that Mikushka is trying to take the relationship to "five," but the hands keep going back to four, as was previously stated.
Oh, and one last thing...